Showing posts with label biology. Show all posts
Showing posts with label biology. Show all posts

Friday, April 22, 2016

Chameleons, Crystals: and Curiosity

Chameleons may be more famous for changing color than for their high-speed tongues: but today I'll be talking about both.
  1. Chameleon Tongues, Mathematically Described
  2. Crystals in Chameleon Skin

Brains, Curiosity, and Being Human


Using our brains is part of being human. So is learning about the universe, and using that knowledge. We're supposed to use our brains. (Catechism of the Catholic Church, 154-159, 2292-2296)

But, particularly if we act without thinking, curiosity can get us killed. I've talked about Georg Wilhelm Richmann before, and why "tickling the dragon's tail" is a bad idea.

Also why Ulysses is in Dante's Malebolge, and it's not because being curious is wrong. (January 23, 2015)

Let's see, what else?

Ethics matter.

'It's for science' isn't an excuse for subjecting humans to lethal experiments: or mistreating animals. I've talked about that before. (March 27, 2015; December 5, 2014)

Basically, science and technology are fine. Ignoring ethics isn't. (Catechism, 159, 2292-2296, 2375-2377, 2414)

1. Chameleon Tongues, Mathematically Described



(From SPL, via BBC News, used w/o permission.)
("The chameleon feeds by snapping out its long tongue"
(BBC News))
"Chameleon's tongue gives up secrets"
Helen Briggs, BBC News (April 20, 2016)

"Scientists have built a mathematical model to explain the secrets of the chameleon's extraordinary tongue.

"It took more than 20 equations to capture mathematically how the reptile's tongue unravels at very high speed to snare insects.

"The model explains the mechanics of the animal's tongue and the inherent energy build-up and rapid release.

"British researchers say the insights will be useful in biomimetics - copying from nature in engineering and design...."
Depending on who you read, chameleons have been around for 60,000,000 years, give or take, or roughly 20,000,000 years. That's how far back we've found various iguana-like fossils.

The odds are good that the critters have been around for a lot longer, and share a common ancestor with iguanids and agamids upwards of 100,000,000 years back.

Somewhere along the line, chameleons acquired their color-changing ability. They're not the only variable-color animals. Quite a few critters go through seasonal color changes, of course; but anoles, squids, octopi, and cuttlefish change quickly.

Back to chameleons: we know of 202 species, not all can change color; they've got zygodactylous feet, which is a fancy way to say two toes point backwards; and they've got weird eyes.

A chameleon eye's lens is convex, not concave like ours. That's not obvious, looking at them, but the way they move their eyes independently of each other is.

Chameleons can swivel their eyes around a whole lot more than we do, which lets them stay still while waiting for their next meal: or avoiding being another critter's food.

Tarsiers have enormous eyes for their size, at least some can turn their heads a full 180 degrees. I'm assuming that's 180 left or right.

Oxford University's professor of mathematical biology Derek Moulton clarified — if that's the right word — what these scientists did:
"...'In mathematical terms, what we've done is we've used the theory of non linear elasticity and captured the energy in these various tongue layers and then passed that potential energy to a model of kinetic energy for the tongue dynamics.'..."
(Helen Briggs, BBC News)
I gather what that means is that the scientists found a set of equations that do a pretty good job of describing what a chameleon's tongue does.

It's a very complicated organ: modified hyoid bones at the core, then about a dozen very thin layers of fibrous material, wrapped in muscles. Energy gets stored in elastic elements — which is what the scientists now understand a bit better.

Heads, Neck Injuries, Getting a Grip, and Designing Robots


We can turn our heads something like 80 degrees left or right: apparently that's about the same for men and women, on average, although men generally have more muscle in our necks.

That may help explain why men aren't quite as likely to have neck injuries. I'd better explain that, considering the preferred reality many folks insist on.

I think humans came in two basic models, male and female: and that this is okay. (May 2, 2012)

That is not even close to yearning for the 'good old days.' I've discussed Addams Family Values, love, and moving forward, before. (January 31, 2016; August 30, 2015; July 12, 2015)

I must believe that we're all created in the image and likeness of God: with free will, masters of our own actions. I must also see all of us as people, with equal dignity: no matter where we are, who we are, or how we act. (Genesis 1:27; Catechism, 360, 1700-1706, 1730-1825, 1932-1933, 1935)

But I don't have to insist that I'm indistinguishable from Elizabeth II, John Krahn, Akihito, or Phumzile Mlambo-Ngcuka. I look a bit like the first two, though: largely because my recent ancestors spent a long time in northwestern Europe.

Less hair and more beard, though, and that's another topic. Topics.

Where was I? Chameleons, eyes, being human. Right.

We've known that chameleons could shoot out their tongues fast and far — and have been learning more about how they manage it. This research could help scientists and technicians design soft, elastic materials for robotics. That's not the scientists' main motive, though. They said their reason for researching was mostly just "scientific curiosity."

More than you probably need (or want) to know about chameleons, tarsiers, and humans:

2. Crystals in Chameleon Skin



(From Alex Hyde/SPL, via BBC News, used w/o permission.)
("The study was conducted on panther chameleons, which are popular pets"
(BBC News))
"Chameleon colours 'switched by crystals' "
Jonathan Webb, BBC News (March 11, 2016)

"Swiss researchers have discovered how chameleons accomplish their vivid colour changes: they rearrange the crystals inside specialised skin cells.

"It was previously suggested that the reptiles' famous ability came from gathering or dispersing coloured pigments inside different cells.

"But the new results put it down to a 'selective mirror' made of crystals.

"They also reveal a second layer of the cells that reflect near-infrared light and might help the animals keep cool...."
Like I said before, (some) chameleons can change color. The real animals are nowhere near as versatile as their cartoon counterparts, though.

Researchers are pretty sure chameleons change color for different reasons: blending in with their surroundings, staying warm or cool, or signalling each other.

Iridophores



(From Teyssier, Saenko, Van Der Marel, Milinkovitch, via BBC News, used w/o permission.)
("A panther chameleon can switch in minutes from camouflage colours to more strident, communicative ones"
(BBC News))
"...Some changes arise from shifting pigments. Tiny packets of the dark dye melanin, for example, can be spread throughout the tendrils of big "melanophore" cells - or gathered into the centre, to lighten the skin again. Many fish and reptiles grow lighter or darker in this way in response to stress, or to match their surroundings.

"Panther chameleons, the subjects of the new study, do this as well. But males can also change between entirely different colours, turning a camouflaged green into a more spectacular yellow, for example, when they see a potential mate or a competitor.

"Until now, many scientists had thought that these changes arose from a similar dispersion trick with yellow or red pigment. The new research suggests this is not the case...."
(Jonathan Webb, BBC News)
Color-changing chameleon skin has a layer of guanine crystals under the outer pigments. The crystals reflect different wavelengths, depending on how they're spaced and arranged: which changes the critters' colors.

Guanine is one of the four main nucleobase in DNA and RNA. We use crystalline guanine as a shampoo additive — for an iridescent look — metallic paints, eye shadow, and nail polish.

The stuff has two tautomeric forms, keto and enol: which matters to folks who make a career or hobby of organic chemistry. My guess is that you're more likely to hear someone mention iambic pentameter: which has more to do with Shakespeare than meters, and that's yet another topic.

Those guanine crystals are in iridophores, a special sort of pigment cell. Here's a photo:


(From M. Milininkovitch, via BBC News, used w/o permission.)
("Inside the 'iridophore' cells of a relaxed chameleon (left) the crystals are tightly packed; excitement causes them to loosen (right)"
(BBC News))

Cool Chameleons



(From M. Milinkovitch, Lanevol.org, via BBC News, used w/o permission.)
("An extra layer of cells that reflect near-infrared wavelengths may help chameleons stay cool in the sun"
(BBC News))
"...Beneath the layer of iridophores that contained a nice, regular lattice of crystals, the team also spotted an additional layer, where the cells were much bigger and more chaotically organised.

"Because that higgledy-piggledy structure reflects near-infrared light particularly well, they believe it might serve to reflect the sun's warming rays and keep the chameleons cool.

"This split appears to be unique to chameleons; other lizards tend to have their crystals arranged in a regular way to give bright colours, or a disorganised way that reflects the heat. With their added layer, chameleons manage to combine the two extremes...."
(Jonathan Webb, BBC News)
Merriam-Webster says "higgledy-piggledy" first showed up in 1598, means "in a confused, disordered, or random manner," and that we don't know its etymology.

Etymology is a word's derivation, entomology is the scientific study of insects, and chameleons eat insect. Insects have compound eyes, some critters with compound eyes living near hydrothermal vents can see infrared.

Quite a few insects can see ultraviolet colors. So could we, at least the wavelengths close to 'visible' light, but the lens of our eye is opaque to ultraviolet. And that's — you guessed it — still another topic.

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Friday, January 29, 2016

Sleep and Being Human

Humans sleep, which shouldn't be surprising. Just about all critters with brains sleep: mammals, birds, reptiles, amphibians, fish — even insects and nematodes experience something like sleep.

Poets and playwrights have written of sleep:
"For in that sleep of death what dreams may come,
When we have shuffled off this mortal coil,
Must give us pause."
("Hamlet," Act III, scene 1; Shakespeare)
Cheerful fellow, Hamlet, and that's another topic.

Aristotle and others had studied sleep, but it wasn't until the 1937 that Alfred Lee Loomis and others began recording and analyzing data from folks hooked up to an electroencehalograph. Or maybe it was 1929.

Either way, we've learned quite a bit since then: and are discovering that there's much more left to learn.
  1. Humans: Wakeful Primates
  2. "How Doth the Little Crocodile"

An Animal: and Human


I'm an animal: a creature with physical form and senses. When I look in a mirror, I see eyes, nostrils, and a mouth; pretty much like most other animals. The hair tells me I'm a mammal, and other characteristics peg me as a primate.

I can decide to act like 'just an animal,' or think about what I do before I act. (Catechism of the Catholic Church, 1951, 1730)

I'm better off if I think before acting, and that's yet another topic. (Catechism, 311, 1730, 1778, 1804, 2339)

I'm a Catholic, so I believe that God is making the universe: and that scientific discoveries are an invitation "to even greater admiration for the greatness of the Creator." (Catechism, 279, 283, 301-308)

If you've read these posts before, you know why I think the universe is billions, not thousands, of years old; Earth isn't flat; Adam and Eve weren't German; poetry isn't science; and thinking is not a sin.

Then there's my take on humility and the universe:
Bottom line, I figure that God gave us brains and expects us to use them. Now, finally, an eye-opening bit if research about sleeping primates.

1. Humans: Wakeful Primates



(From RM Fauna/Alamy, via BBC News, used w/o permission.)
("Gorillas build new sleeping nests each night"
(BBC))
"Why humans need less sleep than any other primate"
Melissa Hogenboom, BBC Earth (January 21, 2016)

"I have always been envious of people who can get by with only six hours' sleep. I prefer eight, sometimes more. I can function on six, but after a few days my brain will be way below full capacity.

"How much sleep we get affects us all. Too much sleep makes us groggy and disorientated. Sleep too little and our mood and concentration suffer. If this carries on it can also cause serious health issues, heightening the risk of diabetes, obesity and high blood pressure.

"Most of us sleep between six to nine hours a night, meaning we spend about a third of our lives asleep. This may seem like a long time, but we actually sleep the least among all the primates – the group that includes monkeys, apes and us.

"So says a new analysis looking at the impact sleep has had on our evolution. The new research suggests that humans have evolved to sleep less, but also to sleep very deeply. This may help explain our success as a species...."
Hogenboom's article starts with Australopithecines, "extinct, close relatives of humans and, with the extant genus Homo, comprise the human clade," as Wikipedia puts it.

I've talked about Carl Linnaeus, taxonomy, and similarly-dry stuff before: also these four-foot tall early members of humanity's family. (May 29, 2015; June 20, 2014)

Australopithecines would have had a hard time trying to blend into a crowd these days. It wasn't just their height — they were around four feet tall for the most part. These folks had way more face and less forehead than today's model.

They had really small brains, too: 500 cubic centimeters; compared to 1300 cubic centimeters, give or take, on average now. I'm inclined to call them "who" instead of "what," though, since they quite likely had a gene that boosted the length and ability of neurons in our brains. (June 20, 2014)

Hogenboom says their bodies were more like other apes than ours are, and she's probably right. The point is that they probably slept in trees, like every other primate except humans.

This is a big deal, since about a million years later our remote ancestors had bodies shaped pretty much like ours: complete with the long legs we use to cover ground, at the expense of agility in trees. It's quite possibly that we started sleeping on the ground around that point.

The good news about that is that folks sleeping on the ground don't have to worry about falling out of a tree. On the other hand, predators had an easier time finding us on the ground. We may or may not have added fire to our toolkit by that time.

Fire and Dreams


The earliest evidence of fire use is about 1,500,000 years old, and that's debatable. I wouldn't be surprised, though, if we learn that this basic tech is goes further back.

Homo erectus apparently made abstract marks, and definitely used tools. 'It happened earlier' is a continuing theme in our increased understanding of our past. (May 29, 2015; December 12, 2014)

Sleeping by a fire and having the Oldowan or Acheulean equivalent of a Bowie knife at hand could make the difference between being some critter's midnight snack, and having fresh meat in the morning.

Small wonder that predators generally steer clear of fires these days, we don't, and that's yet again another topic. Topics. (October 16, 2015; May 29, 2015; January 30, 2015)

Getting back to sleep, which isn't what I meant, primates (except humans) sleep in trees; and sleep a lot. But we dream more.

That's not guesswork or poetry. Dreams and REM sleep go together. Interestingly, our brains sometimes use more energy while dreaming than when we're awake, and I am not going to get snarky about classroom behavior.

Where was I? Sleep, primates, dreams. Right. David Samson and Charles Nunn of Duke University in North Carolina tracked how much primates sleep, and how long each species spends dreaming.

Deep Sleepers



(From Correogsk, via Wikimedia Commons, used w/o permission.)
"...As well as noting how long the animals slept for, they looked at how much time they spent in rapid-eye movement (REM) sleep. This is when we dream, and when our brain consolidates our memories into long-term storage.

"Humans slept the least. The sleepiest primates were grey mouse lemurs and night monkeys, which slept for 15 and 17 hours respectively.

"But in contrast, humans spent the highest proportion of their sleep in an REM state: almost 25%. 'Humans therefore have the deepest sleep of any primate,' says Samson...."
(Melissa Hogenboom, BBC)
These scientists found a pattern: monkeys get a lower percentage of REM sleep than apes, and apes experience REM sleep less than humans. Maybe that's because monkeys sleep on tree limbs, apes build sleeping nests, and humans recently started making innerspring mattresses. Or maybe not.

One more point, and I'll take a look at half-asleep crocodiles.

Folks living in industrialized societies couldn't possibly sleep well, right? I mean, we've got street lights and late-night movies and instant coffee — you get the idea.

In stark contrast, the "noble savage," uncorrupted by decadent civilization — I am not going to wander off on a discussion of 18th century sentimentalism, human nature, and getting a grip. Not now, anyway.

Turns out that in at least three non-industrialized societies folks get by on substantially less sleep than I do: 5.7 to 7.1 hours per night, averaging 6.4 hours. The folks, two hunter-gatherer groups in Africa and one horticultural group in Bolivia, stayed up well after sunset and woke before dawn.

They're generally healthy, and have no more trouble thinking than any other bunch of folks — so apparently they're getting plenty of sleep.

Maybe folks in my part of the world should take a hard look on the quality of our sleep. My experience suggests that making sure the bedroom is completely dark would help, and that's almost another topic.

More:

2. "How Doth the Little Crocodile"



(From Thinkstock, via BBC News, used w/o permission.)
(" 'A little snippy': The team worked with juvenile, 40-50cm saltwater crocodiles"
(BBC News))
"Crocodiles sleep with one eye watching"
Jonathan Webb, BBC News (October 22, 2015)

"Crocodiles can sleep with one eye open, according to a study from Australia.

"In doing so they join a list of animals with this ability, which includes some birds, dolphins and other reptiles.

"Writing in the Journal of Experimental Biology, the researchers say the crocs are probably sleeping with one brain hemisphere at a time, leaving one half of the brain active and on the lookout...."
The scientists haven't studied crocodile brain waves yet, but that step in their research is coming up. What they've done so far is observe the crocs, using infrared light when it's 'dark' in the critters' aquarium room.

Crocodiles are "a little snippy," as La Trobe University's Dr. Lesku said, so they worked with juveniles: 40 to 50 centimeters long.

A one-eye-open sleeping crocodile keeps its open eye on a human, or where the human was last standing; they do the same for other crocodiles, too.

We think of sleeping with both eyes shut as "normal," since that's how we sleep. But sleeping in shifts, one cerebral hemisphere at a time, may be more common. We've observed it in birds, aquatic mammals, and now crocodiles.

"Unihemispheric slow-wave sleep" may have developed independently each time. Or it may be a very old pattern, predating the days when tetrapods branched out to become today's amphibians, reptiles, birds, and mammals.

As I keep saying, there's much more to learn.

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Friday, June 26, 2015

Beavers, Floods, and Yet Another Dire Prediction

Beavers are back in England, which is good news or bad news: opinions differ on that point.

Quite a few folks died when drains blocked up in Nigeria's capital. Then a gas station exploded. There's more rain in the forecast, so their troubles are far from over.

Finally, there's a new doomsday prediction in a brand-new publication. Madagascan lemurs are imperiled: but not, I think, cockroaches, rats — or humans.
  1. British Beavers
  2. Accra, Nigeria: Floods, Fires, and Mass Evictions
  3. Madagascan Lemurs, German Cockroaches

"...And He Found it Very Good...."


The notion that 'spiritual' is good and 'material' is bad arguably has roots in Plato's cave and theory of Forms.

Gnosticism is more recent. It's the idea that the physical world "...is evil, the product of a fall, and is thus to be rejected or left behind...." (Catechism of the Catholic Church, 285)

It's also emphatically not what the Catholic Church teaches. (Catechism, 465)

That hasn't stopped folks from believing that God blundered when making the visible world, more's the pity.

I take my faith seriously, so I can't see the natural world as basically bad:

Thinking: Mandatory


There's an international environmental conference coming toward the end of November, and an American presidential election next year: so I figure we'll see a bumper crop of dire predictions in the next few months. Also folks claiming that agreeing with them is the only way to save the lemurs.

I'll be trying to make sense of what I see: and plan on writing more about environmental and climate issues than I have been. And no, I do not think the sky is falling.

On the other hand, I'm convinced that we've got brains: and are expected to use them.

That's not just my opinion. As a Catholic, I don't have to be a scientist: but I must think.

Faith isn't reason, but faith and reason get along fine. (Catechism of the Catholic Church, 154, 159, 286; "Fides et Ratio," Pope St. John Paul II (September 14, 1998))

Thinking is particularly important when I decide whether something is right or wrong. Having a 'bad feeling' about something can be useful — but "...conscience is a law of the mind...." We're expected to use our brains. (Catechism, 1778)

I've been over that before. (September 7, 2014; December 8, 2013; July 21, 2013)

1. British Beavers



(From BBC News, used w/o permission.)
("There are no plans to attach satellite tags to the beavers just yet"
BBC News)
"England's wild beaver colony has kits"
Claire Marshall, BBC News (June 24, 2015)

"A female from the first wild beaver colony in England for centuries has given birth to at least two young.

"New footage shows the kits being helped through the water by their mother.

"The images taken in Devon by local filmmaker Tom Buckley provide the first evidence of the new arrivals.

"The Devon Wildlife Trust (DWT) said the slowly expanding population would help to provide an insight into their effect on the surrounding River Otter system in east Devon....

"...Beavers were hunted to extinction in England and Wales for their valuable fur and glandular oil during the 12th Century and disappeared from the rest of the UK 400 years later....

"...'This irresponsible programme should never have begun and it won't be long before the substantial sums spent in other European countries in dealing with problems caused by beavers will be required here in the UK.'..."[Angling Trust's Mark Owen]
I don't know how 'official' the Devon Wildlife Trust is. It's a member of the The Wildlife Trusts, another British outfit. The latter's Patron (capital "P") is HRH The Prince of Wales; their President is Simon King OBE, which stands for Order of the British Empire; and one of their vice presidents is a "Sir."

Very British. The Title of Nobility Clause in my country's constitution prohibits the national government from granting noble titles, Article Thirteen is still pending ratification after two centuries, and that's another topic.

The Angling Trust is one of the United Kingdom waterway societies — non-governmental organizations "concerned with the restoration, regeneration and use of the waterways in the United Kingdom." (Wikipedia)

Getting back to the Devon Wildlife Trust, it's a registered charity: intended to safeguard the future of the county's urban, rural, and marine wildlife and its environment. (Wikipedia)

Ducks Unlimited is an equivalent in my part of the world: an international non-governmental organization that's focused on waterfowl habitat conservation. I like their punning motto: "Banding Together for Waterfowl."

On the whole, I'm glad to see non-governmental outfits in conservation work. My guess is that they're more likely to be run by folks who remember why they were set up to begin with: and folks can decide whether or not to support them.

Beavers and "Control Freaks"


About those British beavers? That family on the River Otter isn't the first in the British Isles since the 16th century. The Eurasian beaver has been living in Great Britain at least since sometime in the late-20th or early-21st century.

Some live in enclosed wildlife parks, others on their own on the River Tay and Knapdale area of Scotland. The Devon beavers are the first south of Hadrian's Wall, apparently. There's more detail in Wikipedia.

I don't know enough about the situation to know how much the beavers will affect British waterways. My guess is that folks living in that part of the world will eventually have to manage their beaver populations, since the critters are enthusiastic dam-builders.

For now, though, I rather hope that the "control freaks" leave well enough alone: at least long enough for a wild population to get re-established. ("Stop the control freaks who want to capture England's wild beavers," George Monbiot, op-ed, TheGuardian.com (July 4, 2014))

2. Accra, Nigeria: Floods, Fires, and Mass Evictions



(From Reuters, used w/o permission.)
("Security forces watch as residents burn dwellings in an impoverished neighborhood in Accra, Ghana, June 20, 2015."
Reuters)
"Ghana destroys hundreds of homes in capital in bid to prevent floods"
Matthew Mpoke Bigg, Reuters (June 21, 2015)

"Bulldozers razed hundreds of homes and businesses in the poor Sodom and Gomorrah neighborhood of Ghana's capital on Saturday so the authorities can start widening a lagoon to prevent a repeat of this month's deadly floods.

"Some residents said security forces sprayed them with tear gas after they threw stones to protect their livelihoods from the bulldozers. By evening, thousands were stranded in the rain amid rubble and household goods strewn for more than a mile.

" 'What they have done is not good for us because this is where some of us work and take care of our families,' said scrap metal merchant Muhammed Abdul Karim as he surveyed the wreckage of his shack and the motorized tricycle he uses to haul iron....

"...The government's action carries a political risk. Many locals are from northern Ghana and have supported the ruling party, but some residents burned their homes in protest at the destruction, starting a blaze that raged out of control...."
I wondered about Reuters' lead sentence: "...the poor Sodom and Gomorrah neighborhood of Ghana's capital...." Near the end of the article, this suburb of Accra gets identified as Agbogbloshie. A little more digging, and I found that Newsweek claims the "Sodom and Gomorrah" moniker is what the locals call it.

Newsweek could be right — or not. I don't know. Apparently the place is filthy, with lots of crime: and allegedly-illegal dumping of electronic waste from other countries.

That last claim is what some folks in Seattle, Washington, said. The World Reuse, Repair and Recycling Association says it's an "e-waste hoax," and a Basel Convention/UNEP/EMPA report said there are "...several challenges for Nigeria to manage e-waste...."

I don't know how much of whose story to believe. What does seem certain is that a whole lot of folks lost their homes and employment. That's not good.1

Apparently at least one fire started when someone who was getting kicked out of their own neighborhood set fire to their former home. Whether that was a legitimate way to express dissatisfaction with what was happening — again, I don't know.

Flood control is very important in Nigeria's capital this year. The Reuters article says flooding killed more than 50 folks on the third and fourth of this month, when water couldn't get through blocked drains. The same night, 96 folks who took shelter in a downtown gas station died when the place exploded.

That may be a low-end estimate. Al-Jazeera's report lines up with Reuters, with "at least 90" fatalities. BBC News and Zee News put the death toll at 150 to 200 and 200, respectively. No matter what the numbers are, that's a lot of hurting families and friends.

More:

Nigeria's Capital: Death and Recovery


Taking a close look at Accra's west side on Google Maps, I found the Agbogbloshie Onions Market and Agbogbloshie Lorry Park near Abose-Okai Road.

That part of Accra's metropolitan area is near the confluence of two streams — and I have no idea whether either of those places are still around, or what happened to the folks who worked there.

Maybe Accra's leadership was justified in forcing folks out of their homes so that their neighborhood could be used as a lagoon. I don't know, and am profoundly glad I don't have to make decisions like that.

I'd like to think that families who were evicted will be compensated for their loss — but fear that they will find recovering from this month's disasters very difficult.

More:

3. Madagascan Lemurs, German Cockroaches



(From EPA, via BBC News, used w/o permission.)
("Climate change and deforestation are among the reasons we may be facing an extinction event"
BBC News))
"Earth 'entering new extinction phase' - US study"
BBC News (June 20, 2015)

"The Earth has entered a new period of extinction, a study by three US universities has concluded, and humans could be among the first casualties.

"The report, led by the universities of Stanford, Princeton and Berkeley, said vertebrates were disappearing at a rate 114 times faster than normal....

"...The study - published in the Science Advances journal - cites causes such as climate change, pollution and deforestation...."
Oh-kay. That's interesting. This particular study is in Science Advances, a brand-new open-access journal published by the American Association for the Advancement of Science.

I assume the facts in this study are accurate. Earth's climate is changing, species have been going extinct since life began on this planet, and the last I heard we're in one of Earth's glacial epochs. This isn't our home's most tranquil time. (July 11, 2014; May 8, 2015)

As for the conclusion, as stated?

We're keeping much closer track of critters these days, so some of the apparent spike in the extinction rate might reflect that increasing awareness. Or maybe we are facing a sudden shortage of lemurs.

However, I'm also aware that there's a major election coming in 2016: and the usual weirdness is well under way. The scientists who wrote that study may sincerely believe that humanity's number is up: or maybe they figure that the masses need another dose of panic.

I really don't know.

Extinction, Panic, and Cockroaches


I take environmental concerns seriously.

However, although I'm sure that we need to use our brains — I think we're no more in danger of extinction than the black or brown rat, or the German cockroach.

We're opportunistic omnivores: designed to eat just about anything we can catch and cook; plus whatever fruits; nuts, berries; or, sometimes, bark; the local smörgåsbord offers. (May 9, 2014)

We're not as spectacularly disease-resistant as some critters, but the Black Death didn't do more than slow us down — and that was before we knew about microbes. (April 19, 2015; April 4, 2014)

Don't get me wrong: I realize that the Great Pestilence, as folks called it at the time, brought death and tragedy to Eurasia in wholesale lots. But we survived.

I don't think blind complacency makes sense: but I'm convinced that an equally-blind panic is just as silly.

And that is yet another topic.

Why I'm concerned, but not spooked:
1 Loving neighbors is very important. (Matthew 22:39; Luke 10:27)

Since we're social creatures, we must cooperate and respect individuals. (Catechism, 2238-1889)

This cooperation includes responsibilities of citizens to respect and obey civil leaders — within reason. (Catechism, 2238-2243)

Those in authority have responsibilities, too: which include respecting "...the fundamental rights of the human person ... according to the requirements of the common good...." (Catechism, 2235-2237)

The seventh commandment forbids theft, which has implications regarding private property, economic activity, social justice, and respect for the integrity of creation. (Exodus 20:15; Deuteronomy 5:19; Matthew 5:19; Catechism, 2401-2436)
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Friday, June 19, 2015

Tiny Microbes and the Tree of Life, Big Aliens

Small critters: The University of California, Berkeley, press release calls them "bacteria," but scientists may decide that they should get another label. These tiny microorganisms aren't quite like anything else that's had its DNA analyzed before, so textbooks may need to be rewritten in a few years.

Big aliens: Ever since reporters garbled a 1950s UFO sighting, "little green men" has meant "space alien." We still don't know whether there's life, intelligent or otherwise, elsewhere: but a scientist says that if we've got neighbors, they're probably bigger than we are.
  1. Rearranging the Tree of Life
  2. Earth, Space Aliens, and Perspective

It's a Big Universe


I think that we definitely are alone in the universe: or have neighbors. Right now, we don't know. (November 7, 2014; June 27, 2014)

If we do have neighbors, I'd be astounded if the usual SETI (Search for ExtraTerrestrial Intelligence) assumptions are valid: that our neighbors use modulated electromagnetic transmissions for long-distance communications; and are as incorrigibly chatty as we are. (June 27, 2014)

It's been a while since I went over this, so —

The universe started about 13,798,000,000 years back. Earth formed 4,540,000,000 years ago: give or take about 4,540,000. So far, the oldest traces of life are 3,500,000,000 to 3,700,000,000 years old.

We've been making stone tools for about 2,600,000 years, maybe longer.

We discovered radio waves about 150 years back, and began using them for communications a few decades after that.

Blink, and You'll Miss It


Let's compare how many years before today a few key things happened:
  • 13,798,000,000 - universe starts
  • 4,540,000,000 - Earth forms
  • 3,500,000,000 - life starts
  • 2,600,000 - Oldowan stone tools
  • 151 - Maxwell's radio equations
  • 119 - Marconi's wireless telegraphy
On this scale, 151 years is a 'blink and you'll miss it' sort of interval.

If our neighbors started only a million years before or after we did, they'd be almost exactly our age, in a way: 1/13,798th the age of the universe, or 1/4,540th Earth's age.

If they started making stone tools 1,600,000 years ago, and develop new tech about as fast as we do: their current cutting-edge tech includes almond-shaped stone hand axes. They'll find out about radio waves in another 999,885 years - call it 1,000,000.

On the other hand, maybe they started making stone tools 3,600,000 years back, learned about radio waves while we were learning how to use fire, and are currently doing whatever we'll be doing 1,000,000 years from now.

I don't know what tech we'll have by then: but I'd be surprised and disappointed if talking drums, slit gongs, and the Inmarsat network are the ultimate communication technologies. Another set of surprises may be brewing, and I've discussed quantum entanglement before. (May 3, 2013)

Maybe talking about people being around a million years from now seems odd. Around the time I graduated from high school, the silly notion that science and technology will solve all our problems was being replaced by the equally-silly fear that humanity is doomed.

There's the perennial 'end times Bible prophecy,' too, and that's another topic. (April 19, 2015; January 25, 2015)

My guess is that we'll prove to be at least as durable as rats and scorpions. We're certainly smarter. (January 30, 2015; November 29, 2013)

Accepting Reality


Humility, Catholic style, is accepting reality1 — including scientific discoveries, those invitations to "even greater admiration for the greatness of the Creator." It's also about remembering that God's God and we're not. (Catechism of the Catholic Church, 283, 2540, 2559)

Taking care of this world is part of our job. (Catechism, 373, 2415, 2456)

We need tech to get just about anything done, so it's good that studying this world and developing new tools is part of being human. (Catechism, 2292-2296)

Created in the image of God, we're rational creatures "little less than a god:" with the power and frightening responsibilities that come with our nature. (Genesis 1:26-27, 2:7; Psalms 8:6; Catechism, 355-373, 2402, 2415-2418, 2456)

Forgetting that "little less than a god" isn't "God" gets us in trouble. I've been over that before. (March 29, 2015; December 12, 2014)

But, as I keep saying, Thinking is not a sin. (Wisdom 7:17; Catechism, 35, 159, 1730-1738)

One more thing, about Sacred Scripture — As a Catholic I'm "forcefully and specifically" urged to read the Bible, often. (Catechism, 101-133)

That's not the same as assuming that the Bible was written by a literal-minded American (July 13, 2014)

"Little" Green Men?


Getting back to space aliens, I'm not sure why little green men caught on so quickly. Hauling a net through my memory, I dredged up recollections of silver lamé spandex, tacky sets, and Kronos.

Okay, not all space aliens were runts — although Kronos was a giant robot, not a live alien; the movie was really 'relevant;' and that's yet another topic.

I'll be talking about Fergus Simpson's speculations on how big our non-human neighbors might be, and what sort of planet they'd be from, later.

Before discussing tiny bacteria-like things and big hypothetical space aliens, I'll ramble on about how big humans are.

Shrews, Blue Whales, and Us


Size isn't everything, but it's impressive.2 Maybe that's why lots of folks go to see a zoo's elephant, but not many line up to watch the German cockroach. Then again, not many folks find elephants in their pantry.

Elephants are big, but they're not the biggest animal around. That's the blue whale. Gravity limits how big a land animal can be: which is something Fergus Simpson discusses, but I probably won't. Not this time around.

Some dinosaurs were lots bigger than elephants, but they're not around any more. The big ones avoided equatorial areas for a long time, for reasons that may or may not be what some scientists suggest. Yet again more topics.3

I'll take a quick, not terribly scientific, look at some of today's mammals: mostly how much they weigh, in grams. These numbers are approximate:
  • 170,000,000 - blue whale
  • 5,000,000 - African elephant (male)
  • 2,500,000 - African elephant (female)
  • 500,000 - Kodiak bear (male)
  • 270,000 - Kodiak bear (female)
  • 80,000 - human (male)
  • 60,000 - human (female)
  • 4,500 - domestic cat
  • 2 grams - Etruscan shrew
It looks like we're really small: but this list leaves out a lot of animals. The smallest insect, for example, is probably the Dicopomorpha echmepterygis, measuring 139 micrometers long. A single-celled Paramecium is 50 to 330 micrometers long, depending on species.

Besides, although we're about 169,950,000 grams lighter than a blue whale, we're 1/3,400th as massive. That's still pretty small.

On the other hand, an Etruscan shrew is 1/25,000th as massive as an average human — so we're way bigger than a shrew than we're smaller than a whale: on a logarithmic scale.

That might be more important, subjectively, since I suspect that most folks find it easier to think of quantities in terms of fractions.

Think about it: picking up a six-pound object and a three-pound object, is someone more likely to think 'ah! this is 1.36 kilograms heavier than the other?' Or 'this one's twice as heavy as the other?'

My guess it's the 'twice as heavy' option.

1. Rearranging the Tree of Life



(From Banfield group, via Phys.org, used w/o permission.)
("The new groups of bacteria (CPR) greatly expand the known and characterized phyla (top). These and previously reported new groups of Archaea (DSPANN) show that the Tree of Life is oversimplified."
(Phys.org))
"Newfound groups of bacteria are mixing up the tree of life"
Robert Sanders, Media Relations, Berkeley (June 15, 2015)

"University of California, Berkeley, scientists have identified more than 35 new groups of bacteria, clarifying a mysterious branch of the tree of life that has been hazy because these microbes can’t be reared and studied in the lab.

"The new groups make up more than 15 percent of all known groups or phyla of bacteria, the scientists say, and include the smallest life forms on Earth, microbes a mere 400 nanometers across. The number of new bacterial phyla is equal to all the known animal phyla on Earth.

"The scientists, who recently also identified nine new groups of microbes known as Archaea, see these new additions to life on Earth as a sign that the accepted tree of life – a division into the three domains of eukaryotes, which includes animals and plants, bacteria and Archaea – needs to be revised.

" 'This is a new view of the tree of life,' said lead author Jill Banfield, a professor of earth and planetary science and of environmental science, policy and management. 'These new groups of bacteria and Archaea are changing our understanding of the number and arrangement of branches on the tree of life.'..."
A tip of the hat to Vittoria Patti, on Google Plus, for the heads-up on this news.

When I was in high school, I learned that there were plants and animals, that fungi were either non-photosynthetic plants or something else, and that bacteria didn't quite fit into any of those categories. There were viruses, too.

Folks teaching science and writing textbooks weren't trying to confuse us. Scientists were learning that differences between prokaryotes, organisms without cell nuclei, and eukaryotes, organisms with nuclei, were important.

The old Aristotelian/Theophrastotelian classification of living things into plants and animals has been reviewed and revised a lot since Ernst Haeckel suggested calling some critters that weren't much like plants or animals protista.

Obviously, we didn't have all the answers then. We still don't, but we've learned a bit more.

Carl Woese defined Archaea as a third domain or kingdom for life in 1977: introducing the three-domain system we have now. It's a classification system that divides cellular life into archaea, bacteria, and eukaryote domains.

Archaea and bacteria don't have a cell nucleus. Archaea don't have organelles, either: specialized little sacks inside a cell. Neither do bacteria, for the most part.

Archaea and bacteria look alike, sort of, but archaea are more like eukaryotes, genetically, and have some of the same metabolic pathways we do.

Eukaryotes are organisms with a nucleus and other organells in each cell. Well, most cells.

Erythrocytes, red blood cells, in mammals don't have nuclei or other organelles. The same goes for Batrachoseps salamanders and Maurolicus fish, and that's still another topic.

Plants, animals, and fungi are eukaryotes. We don't know much about the evolution of fungi, since they're easily recycled. The earliest fossil that looks like it might be a fungus is about 1,430,000,000 years old. The earliest fossil fungi that are definitely fungi are in the Rhynie chert, a fossil bed formed some 410,000,000 years ago.


(From Ron Blakey, Paleogeography Library, Colorado Geosystems, Inc., used w/o permission.)
(Earth, about 400,000,000 years back.)

Another thing — the "tree of life" mentioned in the article isn't Yggdrasil, the immense tree in Norse cosmology. Its a metaphor biologists use when discussing how organisms relate to each other. Saying "tree of life" is probably easier than something like "hierarchical affinity diagram."

Previously-Unknown Genes



(From Berkeley Labs, used w/o permission.)
(A cryo-electron tomography image from Berkeley Labs, showing the internal structure of an ultra-small bacteria cell. The scale bar is 100 nanometers.
(Berkeley Labs))
"...'People have seen these bacteria in surveys of many different environments all over the planet, so we’ve known that they are there, and that they are fairly ubiquitous,' [Berkeley graduate student Christopher] Brown said. 'What we didn't know is what the organisms were and what they were capable of doing.'

"About half of all the genes in these 35-plus phyla are new and unlike other known genes. The recognizable genes suggest that most of the bacteria use a simple process of fermentation to make the energy they need, instead of using aerobic or anaerobic respiration like many other bacteria. They also have unusual ribosomes, the multi-protein machines that translate genetic instructions into proteins.

" 'The unusual ribosomes, the small genomes – between 600 and 1,100 genes – the inability to synthesize amino acids and nucleotides, and a consistent metabolic story really connects these bacteria together in a pretty surprising way,' Brown said...."
(Robert Sanders, Media Relations, Berkeley)
Before the 20th century, when we developed molecular genetics as a tool for studying organisms, scientists studied critters by observing how they look and act. For the most part.

Now that we can study genetic code, too, we're learning a lot more about life's long story. For one thing, life is very modular on the sub-cellular level. (February 20, 2015; January 9, 2015)

That's one reason that these newly-analyzed microcritters are so exciting. About half the genes in the 35-plus phyla studied are new, and not like other known genes. What that means, and how these critters fit into the rest of Earth's life — is something we'll be discovering.

2. Earth, Space Aliens, and Perspective



(From Metro, used w/o permission.)
("Alien not to scale"
(Metro))
"If aliens exist then they’re absolutely massive, scientist claims"
Ollie McAteer, Metro.co.uk (April 7, 2015)

"The alien of today would leave Marvin the Martian quaking in his tiny space boots.

"That’s because, according to new research, they’re absolutely massive.

"A study by cosmologist Fergus Simpson, a scientist at the University of Barcelona, concludes that extraterrestrials could weigh up to 300kg (nearly 50 stone), if they exist.

"The theory behind it was spawned through observations of our own planet.

"Here on Earth, larger animals need more resources and are therefore less abundant. Earth is considered a planet dominated by smaller lifeforms – including humans...."
The tone of this Metro, UK, article is thoroughly tongue-in-cheek; and its facts not entirely accurate; but Fergus Simpson's research is real.

"Huge" may be a tad misleading, though — 300 kilograms is about 661 pounds, more than a human: but far from the largest critters on Earth. Simpson didn't say "up to" either, and I'll get back to that.

An American bison, for example, weighs between 318 and 1,000 kilograms; a large Gemsbok weighs 300 kilograms; and so does a six-year-old polar bear. Adult polar bears weigh up to 600 kilograms.

My hat's off to Fergus Simpson, the scientist whose paper sparked that news item, for starting his paper with this insight:
"Earth-like planets are expected to provide the greatest opportunity for the detection of life beyond the Solar System. This notion stems from an assumption that the Earth constitutes a simple random sample amongst inhabited planets...."
("The Nature of Inhabited Planets and their Inhabitants," Fergus Simpson, University of Barcelona (March 27, 2015))
Later, he makes the perhaps-obvious point that there's a big difference between the mass of an entire species, and that of an individual.

An individual ant, for example, is much smaller than a human, but the world's living ants as a whole weigh something like 30 to 300 million tonnes. That's close to 350 million tonnes for humans, but a whole lot less than the 1,000 million tonnes of cyanobacteria. (Biomass (ecology), Global biomass, Wikipedia)

He also mentioned Kleiber's law, a rule-of-thumb relationship between an animal's size and its metabolism.

I'm not sure how either relates to how big people with our sort of intelligence might be, although it's important in figuring out how many individuals of various sizes a given habitat is likely to support.

Finally, although the article said Simpson figured space aliens would be "up to" 300 kilograms — Simpson wrote:
"...The median per-individual body mass is calibrated to 70kg, representing the human species ... which implies a typical advanced species of around 314kg...."
("The Nature of Inhabited Planets and their Inhabitants," Fergus Simpson)
In this context, median means the number halfway between the highest and lowest value: pretty much. So what Simpson was saying was that your typical space alien might be around 314 kilograms — about half bigger, another half smaller. That's pretty close to 300, though.

More:

Size, Brains, and Speculation


Fergus Simpson carefully points out Earth is the only planet we know about that supports life, intelligent and otherwise.

That's a really small sample for speculation about life's limits and what our neighbors might be like: if we have neighbors.

Getting back to ants, size, intelligence, and speculation, recently-published research found that mushroom bodies in some social wasps are smaller than those structures in solitary wasps.

These mushroom bodies are structures in the brains of insects, other arthropods, and some annelid worms. They're important for olfactory memory and learning in most insects: including, presumably, wasps.

Social mammals generally have bigger brains than solitary ones, these researchers say. The working assumption is that cooperating with others takes more brainpower than working alone.

Oddly enough, social wasps have smaller mushroom bodies than their solitary counterparts. The scientists speculated that social wasps might use "distributed cognition:" pooling their brainpower:
That doesn't mean that wasps are people, but I think it hints that if we do have neighbors in the universe — they may not be human. Not even close.

My views about:
1 About humility, and thinking:
"CONSCIENCE: The interior voice of a human being, within whose heart the inner law of God is inscribed. Moral conscience is a judgment of practical reason about the moral quality of a human action. It moves a person at the appropriate moment to do good and to avoid evil (1777–1778). An examination of conscience is recommended as a preparation for the reception of the Sacrament of Penance (1454)."
(Catechism of the Catholic Church, Glossary, C)

"HUMILITY: The virtue by which a Christian acknowledges that God is the author of all good. Humility avoids inordinate ambition or pride, and provides the foundation for turning to God in prayer (2559). Voluntary humility can be described as 'poverty of spirit' (2546)."
(Catechism of the Catholic Church, Glossary, H)

"SIN: An offense against God as well as a fault against reason, truth, and right conscience. Sin is a deliberate thought, word, deed, or omission contrary to the eternal law of God. In judging the gravity of sin, it is customary to distinguish between mortal and venial sins (1849, 1853, 1854)."
(Catechism of the Catholic Church, Glossary, S)
2 The idea of comparing critters based on fractional or logarithmic differences comes from Isaac Asimov's essay, "That's About the Size of It" in:
  • "View From a Height"
    Isaac Asimov (1963)
3 More about Earth's equatorial climate and big dinosaurs during the Late Triassic:
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Marian Apparition: Champion, Wisconsin

Background:Posts in this blog: In the news:

What's That Doing in a Nice Catholic Blog?

From time to time, a service that I use will display links to - odd - services and retailers.

I block a few of the more obvious dubious advertisers.

For example: psychic anything, numerology, mediums, and related practices are on the no-no list for Catholics. It has to do with the Church's stand on divination. I try to block those ads.

Sometime regrettable advertisements get through, anyway.

Bottom line? What that service displays reflects the local culture's norms, - not Catholic teaching.